This gene encodes one of the three alpha chains of type IX collagen, the major collagen component of hyaline cartilage. Type IX collagen, a heterotrimeric molecule, is usually found in tissues containing type II collagen, a fibrillar collagen. This chain is unusual in that, unlike the other two type IX alpha chains, it contains a covalently attached glycosaminoglycan side chain. Mutations in this gene are associated with multiple epiphyseal dysplasia. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for COL9A2. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = COL9A2 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.
| TF | Mean coef | Binding | Outlier | TF→Gene link |
|---|
Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of COL9A2, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.
| Accessibility | Element | Dist. to TSS | Link type | TFs |
|---|---|---|---|---|
| chr1:40,039,712–40,041,155 | 274.9 kb | Distal (>10kb) Multiome | 992 | |
| chr1:40,096,788–40,097,757 | 218.2 kb | Distal (>10kb) Multiome | 852 | |
| chr1:40,161,107–40,161,976 | 154.1 kb | Distal (>10kb) Multiome HiCAR | 954 | |
| chr1:40,257,418–40,258,681 | 57.4 kb | Distal (>10kb) Multiome | 1088 | |
| chr1:40,315,144–40,317,664 | 20 bp | At TSS Multiome | 729 | |
| chr1:40,373,298–40,374,444 | 58.2 kb | Distal (>10kb) Multiome | 747 | |
| chr1:40,394,885–40,396,067 | 80.3 kb | Distal (>10kb) Multiome | 153 | |
| chr1:40,449,758–40,450,645 | 134.7 kb | Distal (>10kb) Multiome | 807 | |
| chr1:40,476,972–40,477,791 | 161.9 kb | Distal (>10kb) Multiome | 683 | |
| chr1:40,508,401–40,509,160 | 193.3 kb | Distal (>10kb) Multiome | 805 | |
| chr1:40,531,425–40,532,089 | 216.2 kb | Distal (>10kb) Multiome | 724 |
Genomic view of the COL9A2 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.